Welcome to the PA family! I carry mine exclusively in the back of my F-150 SuperCrew. It has a 5.5 foot bed, so the tailgate and a bed extender help to support it. I have carried mine "right side up" on several trips up to 2 hours and never had any issues with dents, depressions, etc..
Initially I put a shipping blanket in the bed, but have not done that in quite some time. I use a rachet type strap that I run through the side rails and hook to the rear bed tie-downs. I have one of those thick rubber straps with the s-hook on each end that I use across the rear and secure to either side of the bed extender.
I did find after a few trips that the paint on the bed extender can start to wear and it can develop some rust on the edges where the PA contacts it (loading and unloading). That rust can work it way into the plastic and be tough to remove. I ended up applying some tape to the top of the "T-Bar" and have not had any issues since.
For short trips in my neighborhood to get to one of the 2 ramp/launch areas, I normally just use the rachet strap to hold the PA and do not use the bed extender. I'm in the lake at least once a week and have yet to see any depressions or dents associated with carrying the PA on its keel in the truck. By bed does not have a bedliner or anything in it.
2013 Pro Angler 14 - Dune
2015 Pro Angler 14 - Papaya (soon!!)